In site.py there is the internal function _init_pathinfo() This function builds a set of path entries from sys.path. This is used to avoid duplicate entries in sys.path.
But this function has a check if it is a directory with os.path.isdir(...). All this is fine as long as someone has a .zip file in sys.path or a zipfile subpath. Then the path entry is not part of the set. With this duplicate detection with none directories does not work.

The fix is as simple as removing the os.path.isdir(...) line and fixing the indent. Also the docstring should be modified.

Detected by using this function in a project reusing addsitedir(...) functionality to add another path with .pth processing.